Nano clay mineral particles such as kaolinite — with primary particles typically smaller than 2 µm in size — can cause significant problems in flotation processes and tailings disposal, including the processing of Florida phosphate rock and Canadian oil sands. In this study, the consolidated state of flocculated kaolinite sediment was examined, and high-resolution X-ray microtomography (HRXMT) was applied to describe the structure of the consolidated sediment. Using this tomographic information, the complex geometry of the channel network structure for the consolidated flocs was established for the first time. With the establishment of the experimental channel network structure, permeabilities were estimated by flow simulation using the Lattice Boltzmann method. Results for kaolinite sediment with and without polymer are compared and discussed. Results for flocculated kaolinite sediment in a gravitational field are also presented and discussed. The results show that as polymer dosage increases, the permeability of flocculated kaolinite sediment increases, and as suspension pH increases, the permeability of flocculated kaolinite sediment decreases.